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Archive for February, 2008

Hydroponics solution

Wednesday, February 27th, 2008

I’m going to make up my own hydroponics solution. Looking around the web it is hard to find a site with a recipe.

Here’s one at U of Wisconsin-Madison:

0.4 NH4H2PO4; 2.4 KNO3; 1.6 Ca(NO3)2; 0.8 MgSO4; 0.1 Fe as Fe-chelate; 0.023 B as B(OH)3 [boric acid]; 0.0045 Mn as MnCl2; 0.0003 Cu as CuCl2; 0.0015 Zn as ZnCl2; 0.0001 Mo as MoO3 or (NH4)6Mo7O24; Cl as chlorides of Mn, Zn, and Cu (all concentrations in units of millimoles/liter).

Good information from UIUC

and USD.

More on DNA vs. epigenetic information: the strong case for DNA

Monday, February 25th, 2008

I understand PZ’s point, that the information in DNA is expressed through and requires the cell (cytoplasm, nucleoplasm, etc). But the cell is self-assembling–put a human nucleus in a mouse cell, let it divide a dozen times, (maybe a hundred times), and now you have completely human cell. Cloned animals have epigenetic-derived defects, but I expect their Nth generation offspring will be normal.

Let me push the argument further taking a bacterial cell as the model. In principle, you could express proteins in vitro and combine them with lipids, small molecules, and DNA and reconstitute a cell. It wouldn’t be quite right, but get it close enough that it can divide, let it do so a bunch of times and then the cell will be completely normal.

But which proteins would you express and how would you figure out how to combine them? In principle, you could predict from the DNA sequence the set expressed in a particular environment, relative expression levels, and where they go–membrane, cytoplasm, etc.

True enough, DNA without its cellular environment is not a cell, and in biological systems the DNA is always associated with its cell, but the epigenetic information is mainly derived from the DNA and secondary to it. For the biologist this distinction is meaningless–practically we can’t yet predict epigenetic context from DNA or recreate it from scratch. Biologists describe the epigenetic state, observe it and assay for it.

Modeling cells as computer programs

Sunday, February 24th, 2008

PS Meyers has blog post criticizing a creationist describing organisms as computer programs, and then arguing from incredulity against naturalistic explanations for human development. That’s well and good, the creationist is an idiot, but then Meyers takes it a step further and expresses a dislike of software-type descriptions of development:

The genome is not code, efficient or otherwise. Sure, you can tally up the bits needed to store the sequence in a database, but that is not the same as saying you’ve got the complete information for an organism, or that you have captured the “code” that can be executed to build it.

I’m happy to think of the genome as a program. At the high estimate, 100 million bits (25000 genes * 1000 bps per gene * 1000 bps of regulatory seq per gene * 2 bits per bp) or 12Mb to describe the human genome.

So a fairly small amount of code is enough to generate a person. The small number is clearly enough–it is what humans develop with. The program isn’t written in a bloated computer language. It’s more like hand-tuned (or genetic algorithm-tuned, ha) assembly code, full of GOTO statements and with enough cross connected subroutines to make the block diagram look knotted as a ball of thread.

The size doesn’t seem small in relation to the code. Look at the Mandelbrot Set, 7 bytes to write it down and an incredibly complex result. So clearly a small program can produce a complex result.

PZ considers epigenesis important and a reason to reject the computer program hypothesis as insufficient. Epigenesis is clearly important but I don’t see it as a reason to reject the computer program analogy. The epigenetic information is an expression of the genomic program.

Also, calling the genome a library of components seems too static to me. “Library of subroutines” or “library of services” captures the sense of what is going on better, with different subsets of routines active at any time.

It is interesting to compare computer programs with living organisms, but as this creationist shows it is easy to be mislead (or to mislead) by the analogy. I think any complete description of cellular activity and development will use the concepts used to describe computer programs.

Eclipses and earthquakes

Thursday, February 21st, 2008

In anticipation of last night’s lunar eclipse several sites were trotting out the folklore that there are more earthquakes around the time of an eclipse. It seems like an easy thing to study–graph earthquake frequency over time, see if there are more during eclipses. Eclipses occur every couple of years, more often if you consider partial eclipses and small/medium earthquakes occur daily, so someone must have doen this. Looking around the web, the Goddard Space Flight Center answered a Science Question on this very topic (here):

Earthlings can view two lunar eclipses and two solar eclipses just about every year

It’s known that the tides during a lunar eclipse aren’t significantly different than tides during a full Moon. Each is just another spring tide — the name for tides that occur when the Earth is between the Moon and the Sun. If tides don’t really differ substantially during an eclipse than during regular full Moon or new Moon phases, why should celestial positions effect the Earth’s surface or subsurface features? The answer is that they don’t.

Earthquakes and volcanic eruptions do indeed occur at times of eclipses. But records show that they occur with no greater frequency or power than on days when full Moons or new Moons occur (without eclipses), when all the planets line up on the same side of the Sun or on days when the Moon is in a crescent or gibbous phase. As special as eclipses are, they simply don’t have a known impact on any geophysical phenomena.

And just how common are earthquakes anyway?
The ASK-AN-EARTH-SCIENTIST page by the U of Hawaii Geology and Geophysics Department says:

the Earth has about ten earthquakes of greater than magnitude 5 every day


Tuesday, February 19th, 2008

Humans point. Pointing is instinctive in humans. Babies instinctively point to things and pay attention to pointing. They know it is communication. I saw this neat stuff on a Nova episode on ape learning. It mentioned that chimps don’t understand pointing. It’s strange to watch. They don’t do it instinctively and don’t understand it.

Also, apparently we have selected dogs to understand pointing.

Idea: car pushie

Wednesday, February 13th, 2008

Have you ever had to push your car around? Very hard when it is possible at all. So let’s make a short distance car mover. Here’s one way to do it:

Put the front wheels on remote control dollies. Have one remote control work both dollies. The remote control would send two sets of signals, one for each dolly. The dollies are basically remote control cars with low speed/high torque motors and gearing.built heavily enough to carry the load.

The down side of this is that jacking each wheel would be required to put the dollies in place. Also, if the carts had roller skate sized wheels it would not be able to climb curbs.

The Kinsey Institute site

Monday, February 11th, 2008

Always fascinating, on the sexual practices of Papua New Guinea:

The Dobo, who live on a small island off the coast of the main island, live in constant fear of sorcery from their wives. Because they believe that they are particularly vulnerable during intercourse, Dobo men have to continually weigh their need for sexual gratification against the possibility of sorcery when they try to satisfy their sexual need (Davenport 1997, 126).

Much of it makes for disturbing reading. Papua New Guinea is a terrible place.